The year is 2005. In Alaska's Fox archipeligo, A nuclear weapons disposal facility is attacked and captured by the next-generation special forces group known as "Fox-Hound". They have presented Washington with one demand: "The delivery of the remains of the legendary soldier "Big Boss". Unless the demands are met within 24 hours. A nuclear weapon will be launched.
Former member of Fox-Hound, Solid Snake is called back on duty to take the operation. Instructed by Colonel Roy Campbell to infiltrate the base and rescue two hostages, DARPA Chief Donald Anderson, and the president of Armstech Manufacturing company Kenneth Baker. Snake decides to take the operation.
Snake swims the docks of the base and begins to sneak around, The only up to the ground is an elevator that Snake must wait for to come down. The elevator arrives and Snake takes it up to the helipad. Reaching the ground above, Snake contacts Campbell and is introduced to Mei Ling who has also joined the operation as another of Snake's allies. Campbell, Mei Ling, and Naomi Hunter, chief of Fox-hound's medical staff instruct Snake about the mission and give him a few pieces of advice. Snake notices a Hind D ready to lift off the helipad before beginning the intrusion. From the other side of the helipad, Snake scopes out possible entrys into the building and sees a ventilation duct at the top. Silently Making his way to the duct. Campbell calls and says the F-16s used as a diversion were shot down by the hind. Snake crawls through the duct and recieves a transmission from Survivorlist MacDonnell Miller who has also joined the operation. Snake comes to a halt at a shaft looking down on two soliders holding a conversation regaurding a "woman in the cell".
Snake reaches the top balcony of the building inside and makes his way downstairs to the elevator. Taking it to the 1st floor basement, Snake's soliton radar system shows a green dot (DARPA Chief) flashing in a cell in another room on the floor. Finding a ventilation shaft, Snake crawls to the location of the dot and finds the DARPA chief. Snake learns that the DARPA Chief had no idea of the possible threat of the nuclear launch but informs Snake information that the terrorists have been conducting exercises on a new weapon of mass destruction, Metal Gear. The chief gives Snake information how to stop the launch using PAL keys, but time is running out since the terrorists have found out the chief's password to arm the launch, He tells Snake the president of Armstech has a password as well but hasn't shared it yet. Snake learns where Baker may be held up and decides to look for him. Before leaving the cell, the DARPA chief asks Snake something about "the pentagon" and if he's sure he didn't hear anything about disarming the PAL. All of a sudden, the chief dies a mysterious death which looks like a heart-attack. Coming into contact with Campbell, Snake is beginning to think he is hiding something from Snake. He is then instructed to find Baker before he password is given.
Before leaving the cell. Snake hears a struggle in the next cell over and his cell door mysteriously opens. Snake peaks around the corner to find a knocked-out naked soldier on the floor and a woman dressed in the soldier's outfit draws her gun on Snake. Snake calling the woman a "rookie" for her mishandling of her gun, draws his weapon on her. Three guards enter the room as more storm in, Snake and the woman work together taking them out. Checking if the hall is clear. The woman makes a run for the elevator and Snake chases her. She shoots at him and Snake dives for a corner taking cover. After the elevator doors close and the woman disapears, Snake becomes hallucinated by a ghost complementing the girl. Snake calls Naomi to learn that the ghost was Psycho Mantis, Fox-hounds psychic.
Snake takes the elevator down to the 2nd floor basement where Baker is supposedly hiding. Snake finds a wall painted a different color than the others and uses C4 to blow it up, revealing a hall leading to another cover entrance. Snake finds Baker tied up to a pole with several C4 charges wired to blow if the wire is touched. A man appears out of nowhere and shoots at Snake but misses. The man introduces himself as Revolver Ocelot. Challenging Snake to a duel, he shows him his signature revolver and the two get into a fierce battle. Snake manages to take down Ocelot but as Ocelot prepares to shoot once again, his hand is mysteriously sliced off. The ropes tied to Baker are cut and he falls to the ground as the charges go off. Ocelot picks up his hand and runs off telling Snake they will meet again. Snake notices the invisible force has come to form of a cybernetic ninja. It begins to have a painful spell in its head and runs off disapearing into the wind. Snake helps Baker and learns his password was taken and that he couldn't resist Ocelot's extreme torture, which explains his broken arm. Snake learns from Baker that a woman was brought in when the revolt started and gives Snake a hint on how to contact her. He also learns about an employee, Dr Hal Emmerich of Armstech, who worked on the Metal Gear project and who is being held somewhere on the base. With all information gathered, Snake begins to head out and begin his new objectives. Baker hands Snake an opitical disc with all of Metal Gear's test exercise data saved onto it. Before leaving the president, he dies in the same manner as the DARPA Chief.
Leaving the armory. Snake gets into contact via codec with the woman, Meryl Silverbergh who happens to be the Colonel's niece. They share information about the operation and Meryl explains more statistics of the base, Metal Gear and Dr. Emmerich to Snake. Suggesting they team up, Snake declines Meryl's offer because she's still a rookie. But a story of Meryl's horrific experience in battle causes him to give her another chance. Snake suggests going up ahead to look for Emmerich while Meryl agrees to meet up with them.
Making his way through a vacant canyon towards the storage building, Snake receives a transmission from an unknown caller calling himself "Deepthroat", who warns Snake that there are claymore mines planted under the snow. Carefully making his way through the minefield, Snake encounters a tank being commandeered by Vulcan Ravin. Snake, armed with grenades, lobs them at the tank's gunners shooting at him. Snake manages to disarm the tank and reaches the storage building.
Arriving in the building, Snake finds boxes of Dismantled nuclear warheads carelessly stocked and is instructed not to use any weapons in that area. Reaching the elevator, Snake takes it to the 2nd floor basement where Emmerich is held. A hall filled with gas and an electrified floor halts Snake to proceed. Deepthroat calls once more and tells Snake the only way to disarm the electrified floor is to blow up a transformer in a room off the hall. Snake uses a nikita missile to blow it up and proceeds. Entering another hall, Snake finds it filled with dead soldiers who look like they were cut up by a blade. Entering the door at the end of the hall, Snake finds Emmerich trapped by the Cyborg Ninja. The ninja turns around and has been waiting for Snake and "a final battle to the death". Snake and the ninja endure in a fist fight while Emmerich hides in a locker, scared to death. After the battle, the ninja asks Snake if he knows who he is now. Snake can't belive who it is. The ninja takes off once again and Snake reveals to Campbell that the ninja is "Gray Fox", a former partner turned adversary in Outer Heaven years ago. Naomi chimes in and tells Snake and Campbell about how a medical group resurected Fox in Cybernetic form and that the whole operation was a failure due to all the doctors dying during the operation. Snake prepares himself to meet Fox once again when the time comes.
Snake rescues Emmerich and gathers more information on Metal Gear and how it works. However to Emmerich's knowlege, he had no idea that the terrorists were gonna use Metal Gear to launch a missile. Emmerich finally breaks down about how the curse of nuclear weapons has always been a downfall of his family. Snake gets into contact with Meryl but she is cut off by patrolling guards shooting at her. Snake having no idea how to find her, Emmerich tells him she may be dressed up as a soldier who has "a way of walking". Snake decides to go and find her while Emmerich, using his stealth camouflage prototype, stays out of harms way, giving Snake his codec frequency and his new code name : "Otacon".
Snake reaches the 1st floor basement, scoping out the patrolling guards hoping to find Meryl. Meryl spots him and runs to the womans room as Snake follows her in. Snake and Meryl share information about what they've learned so far and Meryl gives Snake one of the PAL keys used to override the detonation. They decide to go to the communications tower up ahead. Arriving at the commander's room north of the 1st floor basement, Snake and Meryl hear strange music and Meryl begins to fall into a trance. She draws her gun on Snake and is ready to shoot. Campbell quickly calls and tellls Snake that Psycho Mantis is controlling her and he should not harm her. Snake, using a stun grenade, knocks Meryl out while he and Mantis endure in a battle. Mantis uses all the objects in the room to try to take down Snake but is unsucessful. Snake manages to kill him. As Meryl regains consiousness, Snake and Mantis hold a conversation as Mantis slowly dies, showing Snake how their worlds are alike because they are both killers and no one deserves happiness. Before dying, he shows Snake the way to the underground base where Metal Gear is stationed. Snake and Meryl leave the commander's room.
Snake and Meryl find a long, wide passage way towards the communications tower but before moving ahead, Meryl is shot three times by a sniper at the end of the hall. Snake, taking cover at the corner, finds himself ungunned and helpless without a sniper rifle. Otacon tells him that there is a PSG-1 back in the armory where Baker was held. With no other choice, Snake travels all the way back to get the sniper rifle.
Arriving back to the hall, Meryl is nowhere to be found, Snake quickly takes cover and seeks out Sniper Wolf, who is waiting for him. They get into a long battle, but Snake manages to take her down. Running towards the balcony where Wolf was shooting from, she's nowhere to be found. Snake finds the door leading into the tower but is side-tracked by Wolf and her men. Snake is knocked out and is dragged away.
Slowly waking up tied to a torture bed, Snake hears leader of Fox-Hound Liquid Snake, who bears a similarity to Snake, make final plans with Wolf and Ocelot on the nuclear attack. Liquid also receives word that the government has refused to give in to his demands. Ocelot is instructed to torture Snake without killing him like he did with the chief. Wolf and Liquid leave and Ocelot begins the torture. If Snake resists the torture, Meryl will be left alone, but if he submits, she dies. Ocelot sends electricity running through Snakes body four times as Snake manages to resist the torture session. True to his word, Ocelot assures Snake that Meryl will be okay for now.
Locked up in a cell, Snake finds the decomposed body of the DARPA chief laying in the corner of the cell. With time to spare, Snake, while in conversation with Campbell, finds out that he was keeping information from Snake regarding the president's methods of dealing with the situation. Snake then talks to Naomi about her and family to ease himself from the pain. Naomi hesitates in talking about herself or her family. Then Snake finally admits to her that he had no family as well but one man who claimed to be his father... Big Boss. The truth behind Outer Heaven is brought up as they continue to talk about their lives. Thinking of a possible way out, the guard watching the cell runs to the bathroom with a stomach ache. Otacon appears and gives Snake food and a bottle of ketchup and a keycard that'll get him out of the torture room. Otacon also begs of Snake not to kill Sniper Wolf because of the feelings he has for her. The guard leaves the bathroom and Otacon disappeers using his Stealth camo. When the guard comes back, he finds Snake on the ground with blood (ketchup) around him. The guard enters the cell and Snake manages to kill him and escape. Gathering his items and clothes, Snake escapes the torture room and heads back to the Communications tower.
Back at the hall where Meryl was shot, Snake stops for a minute to recollect the thought of her getting shot in front of his eyes. Snake admits to Campbell he wasn't able to protect her and he also tells her the truth why Meryl joined in combat. Master Miller tunes in and tells Snake to not punish himself for what's happened. Naomi then sees a little connection going on between Snake and Meryl. Snake then learns that Naomi's father was in the F.B.I. Ending the conversation, Snake enters the entrance of the tower.
Being spotted by a camera. Snake is chased up the long winding tower by swarming guards trying to stop him. He reaches the top of the stairs stopping the soldiers coming after him. Snake climbs a ladder to the roof of the tower. Out on the roof, Snake reaches the catwalk to tower B but is cut short when small missles take down the giant satellite dish on the top of Tower B, dismantiling the catwalk. Liquid appears in the Hind and Snake takes cover as Liquid tries to kill him. Using a piece of long rope, Snake repels down the side of the tower dodging machine gun fire from the hind. Snake reaches the bottom of the tower to a cat walk which will take him to Tower B.
With no time to waste, Snake enters the second tower and runs down the circular staircase to the bottom but is halted when the stair case is broken. Making it back up to where he was. Otacon appears and Snake asks him to fix the elevator that was broken before that will take him down. While Otacon works on the elevator, Snake heads up to the roof of the tower, ready to take down Liquid.
Liquid is hovering around the top of the tower, and Snake gets ready to fight. Armed with stinger missiles, he manages to take Liquid down and the hind comes crashing to the ground below. Otacon calls Snake and tells him the elevator is working. Snake reaches down to the elevator, but when he steps inside, a loud buzz goes off. Ignoring it, Snakes takes the elevator to the bottom floor. Otacon calls and tells Snake that four stealth prototypes he had housed in his lab have gone missing, and the weight of the elevator felt like someone was holding it. Finally reallizing it, Otacon warns Snake that the guys who took his stealth camos are in the elevator with him. Snakes takes down the soldiers and the elevator reaches the bottom floor of the tower. Snake exits the tower into a wide open snowfield where he is shot at by a sniper.
Otacon calls in to check on Snake and Snake tells him that he's being shot at. Otacon excitedly shouts out "It's Her!!", Snake realizes he's talking about Sniper Wolf and that he seems happy. Otacon then begs him once again to not kill her. Snake reminds him that she's a killer and shot Meryl. Wolf interrupts the transmission and tells Snake that he's next to be dead, as Otacon attempts to make peace between the two. Snake vows to pay her back for Meryl. A final sniper battle takes place and Snake takes Wolf down, shooting her in the lungs.
In her final moments, Wolf tells Snake her life story being raised on a battle field and that she was saved by Big Boss. Ready to go down in glory, she implores Snake to set her free. As Snake is drawing his gun on Wolf's face, Otacon appears crying because he's about to lose the love of his life. When Otacon apporaches her, he turns around and says good-bye, closing his eyes and covering his ears. Snake shoots Wolf, killing her as a pack of wolves howl from a distance. Leaving Otacon to grieve with Wolf, Snake heads for the underground base.
Snake takes an elevator down to the bottom level of the blast furnace, reaching a cold storage area. On the way, Master Miller calls Snake and verifiies the story that Naomi told Snake about her father being in the F.B.I was a lie because of false evidence regarding the story. When he enters the room, a flock of ravens appear and fly around him. Vulcan Raven, now armed with a M60 Mini gun challenges Snake to a final duel. Taking him down with the Nikita launcher, Snake wins the battle and Raven, now dying, chants a sermon. He tells Snake that the DARPA chief he attempted to rescue was not really him, but Decoy Octopus, a master of disguise of Fox-Hound. Snake wants more information about it but Raven tells him to solve the riddle, as the ravens pick off of what remains of Raven.
Master calls back with more info on Naomi but this time, Campbell tunes in and Master tells him the story and the new evidence he's gathered indicating that the woman they think is Naomi, isn't her, and that the really Naomi Hunter died somewhere in the middle east some time ago. Fearing that she might be a spy sent in from Fox-Hound, Campbell has her placed under arrest. Snake, believing that Campbell's hiding something, proceeds to the underground base.
Snake reaches the bottom of the base and sees Metal Gear standing high above him, waiting to be used. Otacon calls Snake and tells Snake that he's hacked into Baker's private files about Armstech and information about Metal Gear. Snake tells him to find out how to stop the launch or to destroy it. Reaching the top of the base. Otacon calls back and gives information to Snake about the missile used to be launched from Metal Gear. The weapon is an unstoppable stealth weapon and has only been computer simulated and the outcome of the destruction could mean the end of the world. Snake reaches the control center where Liquid and Ocelot are talking about a possible designated target and they elaborate more on their future plans. Liquid declares that after the attack, Shadow Moses will be called "Outer Heaven".
Snake also learns about FoxDie, and how it killed off Baker and Decoy Octopus. Meryl is still alive and Liquid tells Ocelot to leave her that way.
Otacon calls Snake back and tells him the secret of the PAL override system using the three keys. Snake only having one of them finds out that he actually has all three of them because the card is made out of a shape memory alloy material. To over-ride the launch, Snake must take the key he has and change the temperature of the key because the process requires in order: a room temperature key, a frozen key, and a hot key, and the keys are to only be used once. Looking through the screen of a hidden surveilance camera. Ocelot seeks Snake and shoots at him. The key flys out of Snake's hand and lands back at the bottom of the base. The doors to the control room lock shut as Liquid watches Snake fight off incoming guards.
Snake makes it down to the bottom and retrieves the key and goes back to the control terminal which is now empty. He puts the key in the room temp. terminal and makes his way to the cold storage area where he fought Raven to freeze the key. After going back and entering the frozen key into the Low temp. terminal, Snake heads to the blast furnace to warm the key. Taking the elevator up to the blast furnace. Naomi secretly calls Snake and tells the truth about her and her assignment. She admits to Snake that Gray Fox is her brother and that she injected Snake with FoxDie in retaliation for his killing. Before continuing, she is cut off by Campbell and is beaten up in the background as Campbell forbids Snake to talk to her.
Arriving back at the control terminal with the key in its hot state. Snake puts the key in the high temp. terminal and Metal Gear suddenly becomes activated. Master calls Snake to thank him for inputing the detonation code and explains that Metal Gear is now unstoppable. He reveals to Snake that the DARPA chief's code was never retrieved and that the threat was never intentional and that Snake was sent in as an ace-in-the-hole to obtain Metal Gear's launch data on the opitcal disk he was carrying. Demanding more information from Master. he tells Snake that he's very close by. Campbell interrupts and tells Snake that the body of Master Miller was found at his home recently, and his transmission signals were coming from inside the base. On the codec screen, "Master" takes off his sunglasses and releases his ponytail, revealing himself to be Liquid who's been playing Snake from the beginning. Suddenly the doors of the control room close and lock up as gas is released to kill Snake. Seconds later, Otacon hacks into security and opens the door for Snake. Snake leaves the room and finds Liquid waiting for him next to the cockpit of Metal Gear.
Liquid reveals more information regarding the operation and Snake being a pawn in it, and how he was being used as a vector to spread FoxDie. But as long as it doesnt kill Snake, then Liquid isn't worried about it. Liquid then gets into specifics about Big Boss's DNA and how the two of them are the Sons of Big Boss with Snake being dominent to Big Boss's genes and Liquid being recessive. The truth for Liquid wanting revenge finally comes out as he jumps into the cockpit of Metal Gear and arms it, leaving Snake to take it down once again.
Armed with Stinger Missles, Snake fires at Metal Gear's weakpoint, the radome. When it finally stops for a couple of seconds, it comes back to function and it moves in on Snake. Fox appears and covers Snake as he takes cover. Fox shoots a laser gun at Metal' Gears Radome twice leaving it dysfunctional for a minute, giving Fox a chance to explain to Snake the reason why Naomi wants revenge, and that he was the one who killed her parents and shortly after took her in as her own flesh and blood. He gives Snake a message to tell her that it was him who did it and gives him a box of Stingers to use against Metal Gear. Fox declares that he'll stop Metal Gear for good and in the process gets his arm cut off by Metal Gear's Laser. Jumping to a ledge. Liquid drives Metal Gear's beak into Fox, violently crushing him into the wall. Grabbing his laser gun, Fox shoots at the radome as Liquid yells to Snake, destroying it. With Metal Gear now automatically disabled, Liquid uses the manuel form of Metal Gear and finishes off Fox by pulling him down the ground and stomping on him. Snake is left to watch Fox die for good. Snake goes in one more round with Metal Gear as Liquid Pilots it continuing to try to kill Snake. Snake launches Stingers into the cockpit and destroys Metal Gear for good, but the explosion sends Snake into a hardwall knocking him out.
Liquid appears out of the wreckage of Metal Gear as Snake slowly regains consiousness. More truths about his plan of hostile takeover and his intentions with Big Boss's DNA come clear to Snake. It is revealed that the genome army patrolling the base are also to be the Sons of Big Boss using his Genetics to make the army, "Next- Generation Special Forces". After disarming Snake of all his weapons, Liquid points to Meryl laying tied up and uncousious on the back of Metal Gear with a bomb set to go off. Liquid gives Snake a chance to call Campbell to learn what the pentagon is about to do.
Campbell tells Snake that the Secretary of Defense has taken active lead of the operation and has ordered the pentagon to launch a bomb on Shadow Moses to vaporize the evidence and people who were involved in the Metal Gear project. Campbell insures Snake that he'll stop the nuclear strike or at least delay the chain of command to give Snake a chance to escape. He finally admits the truth that Meryl was brought in as bait to manipulate him and force him to cooperate in keeping vital secrets from Snake. Campbell is then cut off and knocked out, Mei ling scared tries to tell Snake what just happened but then Secretary Of Defense, Jim Houseman comes on telling Snake that Campbell's been arrested for treason, and leaking information. He reveals that the bombing of the island will be covered up by a story involving the terrorist's exploding a nuclear device. Snake defends the sakes of the people of the island and tells him that Houseman didn't really mean to kill the chief after all. Houseman then tells Snake if he hands over the disc holding Metal Gear's test data that everyone will be okay. But Snake tells him he doesn't have it. Houseman then tells Snake that he and Liquid will die soon and the country's dark little secret will be forgotten for good.
With time winding down of the bomb attack, Liquid challenges Snake to a fight with Bare fists on top of Metal Gear's head. If Snake wins, he has a chance to save Meryl for a short time. They begin to fight for a while and Snake manages to throw Liquid off of Metal Gear sending him 25 stories to the ground below.
Snake reaches Meryl who awakens slowly and Snake defuses the bomb next to her. Sharing a moment with Meryl for their somewhat success, he tells her the entire base is about to blow but they plan to attempt the escape. Otacon calls and congratulates Snake on destroying Metal Gear and hears about the bombing run. As Otacon decides to stay for a little bit longer to clear his head and to turn away from the past that has haunted him, They end their conversation for what looks like the last time.
The base begins to rumble and Snake and Meryl get off Metal Gear and run for a garage sitting next door. They find a jeep with a machine gun mounted in the back. Meryl hops in the driver's seat as the rest of the genome soldiers come after them. Getting the jeep to start, Meryl drives by Snake as he hops in the back taking control of the mounted gun. They drive down a long tunnel as they fight off more soldiers trying to stop them. After they kill off the remaining army, Liquid pursues them in another jeep with a famas in his hand. Liquid and Snake exchange fire as the jeeps avoid being hit. At the end of the tunnel, they reach daylight but when they reach the ice covered road, the jeeps turn over leaving Snake and Meryl trapped. Looking around to find Liquid, Snake assumes he's dead, but then Liquid appears from the passenger side of his turned over jeep drawing his FA-MAS on Snake. Snake and Meryl look at him, before he pulls the trigger, Liquid staggers and falls to the ground inducing what looks like the effects of FoxDie. Snake thinks if Liquid died from it, he'll probebly be next.
Campbell suddenly calls and tells Snake that Houseman has been arrested and the whole operation was led by him acting alone. The bombing has been cancelled and Campbell learns that Meryl's okay. He apoligizes to Snake for the secrets he's kept from him during the operation. He tells Snake that there's a snow mobile hiding in a cave not far from their location and they can use it to escape. Thinking they won't ever meet again, they say there good byes but Snake promises him a visit sometime soon. Snake then asks about FoxDie but Campbell tells him that Naomi wants to talk to him about it. Snakes tells Naomi about her brother and the last message he had for her and that he is now a hero for saving the world. She begins to cry at the fact they she never had a chance to say good bye or to see him one last time. Snake changes the subject asking about FoxDie and that it killed Liquid. He asks her how much time he has left, but Naomi just tells him "Everyone dies when their time's up", leaving Snake with the fact that he was never injected with FoxDie in the first place.
Snake and Meryl emerge from the jeep and begin to walk down the cliff to their snow mobile. They hop on and discuss the future their lives have in store for them. Meryl gives Snake a bandana she had with her and they ride off into the sunrise.
Ocelot is on the line with someone explaining the aftermath of the operation,that no one knows his true identity, and that he's recovered Metal Gear's test data. He bids thanks and farewell to "Mr. President"